SubgeneViewer is a plugin in development for the network visualization software Cytoscape. Slated to be released as a part of GenMAPP-CS beta in late 2012, SubgeneViewer allows users to examine the complete exon, junction and intron structure of a gene and view associated exon expression data. Annotations for SubgeneViewer are derived from AltAnalyze during the database build process.[Salomonis2009]
SubgeneViewer 2.0 will be implemented with data from RNASeq experiments in mind. Specifically, novel exon and junction information will be included in the existing gene model (meta-transcript view) and new view analogous to that provided in DomainGraph will be implemented (multi-transcript view). The multi-transcript view will allow users to visualize the impact of alternative exon and junction expression protein domain, motifs and microRNA binding sites. Both known and novel transcripts detected in a user's experiment will be supported (see below mock-up).
SubgeneViewer Mock-up: Mock-up of the (A) meta-transcript and (B) multi-transcript views in SubgeneViewer 2.0.